This is a series of invited colloquiual lectures provided by top researchers in the field of systems biology, theoretical and computational biology, bioinformatics and related fields of applied mathematics and computer science. The series is prepared in collaboration with Global Change Research Centre AS CR as a part of the ESF co-funded project CyanoTeam. The project is associated with an international network CyanoNetwork.

Lectures run irregularly during the academic year with respect to the time schedule provided on this web page. Each of the lectures will be announced at least one week in advance.

Although (bio)chemical reaction networks have been under intensive study
during the last decades, a general theoretical formalism capturing both the
algebraic and the energetic properties of the underlying chemistry is still
missing.

The structural change of molecules during chemical reactions can
conveniently be modeled as graph rewrite, if the participating molecules
are treated as edge and vertex labeled graphs. The graph grammar approach
to chemical transformation captures nicely the algebraic structure of
chemical transformation i.e. the fact that reacting molecules yield novel
molecules while retaining the possibility to assign physico-chemical
properties to the molecules via the arsenal of chemoinformatics methods.

With a constructive method to expand arbitrary chemical transformation
space at hand, the focus of interest shifts to the question of finding sub
network with particular properties, e.g. exhibiting auto-catalytic
behavior, in these spaces. The problem of finding such sub networks can be
formulated as a network flow problem on the underlying hyper-graph which
can be solved using integer linear programming techniques.

Next speaker is planned to be Vashti Galpin, Ph.D., a well-acclaimed computer scientist from University of Edinburgh with many experiences in application of process algebras to systems biology. The talk is planned for February/March 2013.